Whats-New-GPML2021.html Updates Compact IDs

[DeniseSl22]

Regarding the documentation below:

• [ ] How can people register new data sources, from within PV? (I actually don't think we would want that...)
• [x] "is given priority"; how? For the dropdown menu? Or by adding "CHEBI:12345", chebi is automatically selected as Database?
• [ ] what does "Additionally, Xref is added for the Pathway." mean?

[mkutmon]

1. If a datasource is in the GPML file that is not in BridgeDb, it will be added in the session and not break anything. Linkouts and mappings won't work but the Xref can simply be displayed. There is no reason why we shouldn't do that. Those datasources will not be available in the dropdown boxes and we might decide to not allow pathways with unregistered datasources to WikiPathways but that's a different discussion.

2. If a compact identifier prefix for a datasource is given, we will write out the prefix. Some datasources in BridgeDb do not have a registered prefix in identifiers.org. For those, we will write out the full name or system code.

3. A pathway can now also have an Xref element (see example). We did not store that information in the GPML before but we can do that now.

Hope that answers those questions?

[DeniseSl22]

1. Okay, adding it to the GPML itself sounds like an option, if people can't upload it directly to WPs indeed. And I assume this is more on the implementation side of PV (not the schema), but if this new datasource is saved locally in the session, will PV then provide it as an option for other DataNodes (to avoid various spellings of one and the same database name)? And, can people add multiple unknown databases, or just 1 (as is now the case when loading a BridgeDb file with more then 1 unknown datasource).
2. Okay, understood :)
3. So this means for the PW as a whole (not PW Nodes)? That was a bit confusing for me (and the example given does not provide the correct context to understand this either).